To demonstrate the utility of coral skeletons as a recorder of nitrate dynamics in the surface ocean, we collected coral skeletons of Porites lobata and determined their nitrogen isotope composition (δ15Ncoral) from 2002 to 2006. Skeletons were collected at Okinotori Island in southwestern Japan, far from any sources of terrestrial nitrogen. Nitrogen isotope compositions along the growth direction were determined at 800 μm intervals (∼1 month resolution) and compared against the skeletal carbon isotope composition (δ13Ccoral-carb), barium/calcium ratio (Ba/Ca), and Chlorophyll-a concentration (Chl-a). From 2002 to 2004, ratios of the δ15Ncoral varied between +0.8 and +8.3‰ with inverse variation to SST (r = −0.53). Ba/Ca ratios and Chl-a concentrations were also observed to be high during seasons with low SST. These results suggested that the vertical mixing that occurs during periods of low SST carries nutrients from deeper water (δ15NDIN; +5∼+6‰) to the sea surface. In 2005 onward, δ15Ncoral and Ba/Ca ratios also had positive peaks even in high SST during periods of transient upwelling caused by frequent large typhoons (maximum wind speed 30 m/s). In addition, low δ15Ncoral (+0.8∼+2.0‰) four months after the last typhoon implied nitrogen fixation because of the lack of typhoon upwelling through the four years record of δ15Ncoral. Variations in the δ13Ccoral-carb and δ15Ncoral were synchronized, suggesting that nitrate concentration could control zooxanthellae photosynthesis. Our results suggested that δ15Ncoral holds promise as a proxy for reconstructing the transport dynamics of marine nitrate and thus also a tool for estimating nitrate origins in the tropical and subtropical oceans.